./run-asm-pipeline.sh -r 20 --sort-output --build-gapped-map -i 1000 /oak/stanford/groups/akundaje/marinovg/genomes/Chromerida/Chromera_velia_CCMP2878-CDMZ01/bowtie-indexes/CDMZ01.fa /oak/stanford/groups/akundaje/marinovg/papers/2026_Chromera_Hi-C/2026-01-16-Ultima-run-Chromera/juicer-L1273+L4897-Chromera_velia-Hi-C/aligned/merged_nodups.txt &